GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Burkholderia phytofirmans PsJN

Best path

BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, LRA1, LRA2, LRA3, LRA5, LRA6

Also see fitness data for the top candidates


Overview: Rhamnose utilization in GapMind is based on MetaCyc pathway I via L-rhamnulose 1-phosphate aldolase (link), pathway II via 2-keto-3-deoxy-L-rhamnonate aldolase (link), and pathway III via 2,4-diketo-3-deoxyrhamnonate hydrolase (link).

22 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component BPHYT_RS34250
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component BPHYT_RS34245 BPHYT_RS28215
BPHYT_RS34240 L-rhamnose ABC transporter, permease component BPHYT_RS34240 BPHYT_RS28210
LRA1 L-rhamnofuranose dehydrogenase BPHYT_RS28235 BPHYT_RS30440
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase BPHYT_RS34230 BPHYT_RS28240
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BPHYT_RS28250 BPHYT_RS04770
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase BPHYT_RS34210 BPHYT_RS28740
Alternative steps:
aldA lactaldehyde dehydrogenase BPHYT_RS09875 BPHYT_RS09900
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase BPHYT_RS28580 BPHYT_RS31860
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase BPHYT_RS24135 BPHYT_RS28905
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase
rhaM L-rhamnose mutarotase BPHYT_RS28225
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) BPHYT_RS28210 BPHYT_RS25825
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) BPHYT_RS28205 BPHYT_RS16055
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS BPHYT_RS28200 BPHYT_RS25795
rhaT L-rhamnose:H+ symporter RhaT
rhaT' L-rhamnose ABC transporter, ATPase component RhaT BPHYT_RS28215 BPHYT_RS27185
tpi triose-phosphate isomerase BPHYT_RS06610 BPHYT_RS16270

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory